Related references
Note: Only part of the references are listed.Computational modeling of in vivo and in vitro protein-DNA interactions by multiple instance learning
Zhen Gao et al.
BIOINFORMATICS (2017)
gkmSVM: an R package for gapped-kmer SVM
Mahmoud Ghandi et al.
BIOINFORMATICS (2016)
Classifying and segmenting microscopy images with deep multiple instance learning
Oren Z. Kraus et al.
BIOINFORMATICS (2016)
Convolutional neural network architectures for predicting DNA-protein binding
Haoyang Zeng et al.
BIOINFORMATICS (2016)
Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks
David R. Kelley et al.
GENOME RESEARCH (2016)
Predicting Hub Genes Associated with Cervical Cancer through Gene Co-Expression Networks
Su-Ping Deng et al.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2016)
ChIP-PIT: Enhancing the Analysis of ChIP-Seq Data Using Convex-Relaxed Pair-Wise Interaction Tensor Decomposition
Lin Zhu et al.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2016)
Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences
Matthias Siebert et al.
NUCLEIC ACIDS RESEARCH (2016)
DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences
Daniel Quang et al.
NUCLEIC ACIDS RESEARCH (2016)
WELDON: Weakly Supervised Learning of Deep Convolutional Neural Networks
Thibaut Durand et al.
2016 IEEE CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION (CVPR) (2016)
Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data
Ralf Eggeling et al.
BMC BIOINFORMATICS (2015)
Mining the bladder cancer-associated genes by an integrated strategy for the construction and analysis of differential co-expression networks
Su-Ping Deng et al.
BMC GENOMICS (2015)
A Two-Stage Geometric Method for Pruning Unreliable Links in Protein-Protein Networks
Lin Zhu et al.
IEEE TRANSACTIONS ON NANOBIOSCIENCE (2015)
Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
Babak Alipanahi et al.
NATURE BIOTECHNOLOGY (2015)
Predicting effects of noncoding variants with deep learning-based sequence model
Jian Zhou et al.
NATURE METHODS (2015)
Varying levels of complexity in transcription factor binding motifs
Jens Keilwagen et al.
NUCLEIC ACIDS RESEARCH (2015)
Quantitative modeling of transcription factor binding specificities using DNA shape
Tianyin Zhou et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Prediction of Protein-Protein Interactions Based on Protein-Protein Correlation Using Least Squares Regression
De-Shuang Huang et al.
CURRENT PROTEIN & PEPTIDE SCIENCE (2014)
A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data
Yaron Orenstein et al.
NUCLEIC ACIDS RESEARCH (2014)
Normalized Feature Vectors: A Novel Alignment-Free Sequence Comparison Method Based on the Numbers of Adjacent Amino Acids
De-Shuang Huang et al.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2013)
Evaluation of methods for modeling transcription factor sequence specificity
Matthew T. Weirauch et al.
NATURE BIOTECHNOLOGY (2013)
LSE: A Novel Robust Geometric Approach for Modeling Protein-Protein Interaction Networks
Lin Zhu et al.
PLOS ONE (2013)
A General CPL-AdS Methodology for Fixing Dynamic Parameters in Dual Environments
De-Shuang Huang et al.
IEEE TRANSACTIONS ON SYSTEMS MAN AND CYBERNETICS PART B-CYBERNETICS (2012)
ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions
Terrence S. Furey
NATURE REVIEWS GENETICS (2012)
Molecular Pattern Discovery Based on Penalized Matrix Decomposition
Chun-Hou Zheng et al.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2011)
A Linear Model for Transcription Factor Binding Affinity Prediction in Protein Binding Microarrays
Matti Annala et al.
PLOS ONE (2011)
Tumor Clustering Using Nonnegative Matrix Factorization With Gene Selection
Chun-Hou Zheng et al.
IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE (2009)
Diversity and Complexity in DNA Recognition by Transcription Factors
Gwenael Badis et al.
SCIENCE (2009)
A Constructive Hybrid Structure Optimization Methodology for Radial Basis Probabilistic Neural Networks
De-Shuang Huang et al.
IEEE TRANSACTIONS ON NEURAL NETWORKS (2008)
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
Raja Jothi et al.
NUCLEIC ACIDS RESEARCH (2008)
Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
Laura Elnitski et al.
GENOME RESEARCH (2006)
Independent component analysis-based penalized discriminant method for tumor classification using gene expression data
De-Shuang Huang et al.
BIOINFORMATICS (2006)
An introduction to ROC analysis
Tom Fawcett
PATTERN RECOGNITION LETTERS (2006)
Finding short DNA motifs using permuted Markov models
XY Zhao et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2005)
DNA binding sites: representation and discovery
GD Stormo
BIOINFORMATICS (2000)